##### define plotting functions
fitplot <- function(xvars,coefs,year,truth,title,ylabel) {
	fitline <- xvars%*%coefs
	fit <- data.frame(year=year,fit=fitline,truth=truth,error=(fitline-truth))

	plot_base <- ggplot(data=fit, aes(x=year))
	plot_fitplot <- plot_base + geom_point(aes(y=truth),size=1.1) +
							geom_line(aes(y=fit),size=0.9,linetype="dashed", color="blue") +
							theme_bw() + ggtitle(paste(title)) +
							ylab(paste0(ylabel))	+
				theme(text=element_text(family="Helvetica",size=15),
					axis.text.x=element_text(family="Helvetica",size=15),
					axis.text.y=element_text(family="Helvetica",size=15),
					plot.title=element_text(family="Helvetica",size=15) )
	plot_error <- plot_base + geom_line(aes(y=error),size=0.9) +
						geom_hline(yintercept=0,linetype="dashed") +
						theme_bw()	+
				theme(text=element_text(family="Helvetica",size=15),
					axis.text.x=element_text(family="Helvetica",size=15),
					axis.text.y=element_text(family="Helvetica",size=15),
					plot.title=element_text(family="Helvetica",size=15) )

	grid.arrange(plot_fitplot,plot_error,nrow=2)
}

nls_fitplot <- function(xvars,coefs,year,truth,title,ylabel) {
	fitline <- xvars[,1]*(1 - exp(-coefs[1]*xvars[,1] -coefs[2]*xvars[,2]))
	fit <- data.frame(year=year,fit=fitline,truth=truth,error=(fitline-truth))

	plot_base <- ggplot(data=fit, aes(x=year))
	plot_fitplot <- plot_base + geom_point(aes(y=truth),size=1.1) +
							geom_line(aes(y=fit),size=0.9,linetype="dashed", color="blue") +
							theme_bw() + ggtitle(paste(title)) +
							ylab(paste0(ylabel))	+
				theme(text=element_text(family="Helvetica",size=15),
					axis.text.x=element_text(family="Helvetica",size=15),
					axis.text.y=element_text(family="Helvetica",size=15),
					plot.title=element_text(family="Helvetica",size=15) )
	plot_error <- plot_base + geom_line(aes(y=error),size=0.9) +
						geom_hline(yintercept=0,linetype="dashed") +
						theme_bw()	+
				theme(text=element_text(family="Helvetica",size=15),
					axis.text.x=element_text(family="Helvetica",size=15),
					axis.text.y=element_text(family="Helvetica",size=15),
					plot.title=element_text(family="Helvetica",size=15) )

	grid.arrange(plot_fitplot,plot_error,nrow=2)
}

fitplot_noerror <- function(xvars,coefs,year,truth,title,ylabel) {
	fitline <- xvars%*%coefs
	fit <- data.frame(year=year,fit=fitline,truth=truth,error=(fitline-truth))

	plot_base <- ggplot(data=fit, aes(x=year))
	plot_fitplot <- plot_base + geom_point(aes(y=truth),size=1.1) +
							geom_line(aes(y=fit),size=0.9,linetype="dashed", color="blue") +
							theme_bw() + ggtitle(paste(title)) +
							ylab(paste0(ylabel))	+
				theme(text=element_text(family="Helvetica",size=15),
					axis.text.x=element_text(family="Helvetica",size=15),
					axis.text.y=element_text(family="Helvetica",size=15),
					plot.title=element_text(family="Helvetica",size=15) )

	plot_fitplot
}

nls_fitplot_noerror <- function(xvars,coefs,year,truth,title,ylabel) {
	fitline <- xvars[,1]*(1 - exp(-coefs[1]*xvars[,1] -coefs[2]*xvars[,2]))
	fit <- data.frame(year=year,fit=fitline,truth=truth,error=(fitline-truth))

	plot_base <- ggplot(data=fit, aes(x=year))
	plot_fitplot <- plot_base + geom_point(aes(y=truth),size=1.1) +
							geom_line(aes(y=fit),size=0.9,linetype="dashed", color="blue") +
							theme_bw() + ggtitle(paste(title)) +
							ylab(paste0(ylabel))	+
				theme(text=element_text(family="Helvetica",size=15),
					axis.text.x=element_text(family="Helvetica",size=15),
					axis.text.y=element_text(family="Helvetica",size=15),
					plot.title=element_text(family="Helvetica",size=15) )
	plot_fitplot
}


# Multiple plot function: taken from http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_(ggplot2)/
#
# ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
# - cols:   Number of columns in layout
# - layout: A matrix specifying the layout. If present, 'cols' is ignored.
#
# If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
# then plot 1 will go in the upper left, 2 will go in the upper right, and
# 3 will go all the way across the bottom.
#
multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
  library(grid)

  # Make a list from the ... arguments and plotlist
  plots <- c(list(...), plotlist)

  numPlots = length(plots)

  # If layout is NULL, then use 'cols' to determine layout
  if (is.null(layout)) {
    # Make the panel
    # ncol: Number of columns of plots
    # nrow: Number of rows needed, calculated from # of cols
    layout <- matrix(seq(1, cols * ceiling(numPlots/cols)),
                    ncol = cols, nrow = ceiling(numPlots/cols))
  }

 if (numPlots==1) {
    print(plots[[1]])

  } else {
    # Set up the page
    grid.newpage()
    pushViewport(viewport(layout = grid.layout(nrow(layout), ncol(layout))))

    # Make each plot, in the correct location
    for (i in 1:numPlots) {
      # Get the i,j matrix positions of the regions that contain this subplot
      matchidx <- as.data.frame(which(layout == i, arr.ind = TRUE))

      print(plots[[i]], vp = viewport(layout.pos.row = matchidx$row,
                                      layout.pos.col = matchidx$col))
    }
  }
}
